Extract gene_id and protein_id from .gtf file to create a list with them

Question

[Eduardo Oñate]

Hi everyone!

I'm trying to create a list with de gene_id and respective protein_id from a .gtf file, I want to extract de information using a simple line code. I tried using this command:

grep -o 'gene_id "[^"]*"\|protein_id "[^"]*"' file.gtf | paste - - > lista_genes_proteins.txt

But the paste results in the list are not correct. Does anyone know how I can do this? Can help me, please? Thanks.

[GenoMax]

You can use AGAT toolkit to do this properly: https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_attributes.html

[Eduardo Oñate]

Thanks! I resolve it using a different command line and sublime text to edit the text.

I use this command line:

grep -w 'CDS' GCF_003086295.2_arahy.Tifrunner.gnm1.KYV3_genomic.gtf| cut -f9 > columna_9.txt

and use sublime text to edit the file columna_9.txt, It works!.

thanks for taking the time to answer.